MolNFT v1 · #98632 · protein + RNA
Crystal structure of 30S ribosomal subunit from thermus thermophilus
4LF4 · 16S rRNA: “Crystal structure of 30S ribosomal subunit from thermus thermophilus”. X-ray diffraction, 4 ligands (LLL, MG, K), 20 pockets (best druggability 0.89). MolNFT v1 #98632 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4LF4
- Type
- protein + RNA
- Length
- 3,903 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; Ribosomal protein S2; Ribosomal protein S3; Ribosomal protein S4; Ribosomal…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, F6DEQ7, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- LLL, MG, K, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 21 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1513 | — | — |
| B | Ribosomal protein S2 | protein | 235 | 46% helix, 13% strand | P80371 |
| C | Ribosomal protein S3 | protein | 206 | 41% helix, 22% strand | P80372 |
| D | Ribosomal protein S4 | protein | 208 | 39% helix, 9% strand | P80373 |
| E | Ribosomal protein S5 | protein | 150 | 29% helix, 41% strand | Q5SHQ5 |
| F | Ribosomal protein S6 | protein | 101 | 28% helix, 48% strand | Q5SLP8 |
| G | Ribosomal protein S7 | protein | 155 | 55% helix, 9% strand | P17291 |
| H | Ribosomal protein S8 | protein | 138 | 30% helix, 34% strand | Q5SHQ2 |
| I | Ribosomal protein S9 | protein | 127 | 32% helix, 20% strand | P80374 |
| J | Ribosomal protein S10 | protein | 98 | 14% helix, 28% strand | Q5SHN7 |
| K | Ribosomal protein S11 | protein | 119 | 28% helix, 28% strand | P80376 |
| L | Ribosomal protein S12 | protein | 124 | 8% helix, 27% strand | F6DEQ7 |
| M | Ribosomal protein S13 | protein | 118 | 51% helix, 2% strand | P80377 |
| N | Ribosomal protein S14 | protein | 60 | 30% helix, 12% strand | Q5SHQ1 |
| O | Ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | Q5SJ76 |
| P | Ribosomal protein S16 | protein | 83 | 22% helix, 33% strand | Q5SJH3 |
| Q | Ribosomal protein S17 | protein | 104 | 14% helix, 42% strand | Q5SHP7 |
| R | Ribosomal protein S18 | protein | 73 | 38% helix, 7% strand | Q5SLQ0 |
| S | Ribosomal protein S19 | protein | 80 | 26% helix, 19% strand | Q5SHP2 |
| T | Ribosomal protein S20 | protein | 99 | 73% helix, 0% strand | P80380 |
| U | Ribosomal protein thx | protein | 24 | 25% helix, 0% strand | Q5SIH3 |
Ligands and binding sites
- LLL · (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-diamino-3-((2R, 3R,6S)-3-amino-6-(aminomethyl)-tetrahydro-2H-pyran-2-yloxy)-2-hydroxycyclohexyloxy)-5-methyl-4-(methylamino)-tetrahydro-2H-pyran-3,5-diol · ligand · chains A
- MG · Magnesium ion · metal · 153 copies · chains A, N, P, E, L, T, K, M, U, Q, B, C, D, F, H, J
- K · Potassium ion · metal · 10 copies · chains A, E
- ZN · Zinc ion · metal · 2 copies · chains D, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.89 | 0.91 | 87 | MG |
| 2 | 1080 | 0.86 | 0.88 | 92 | MG |
| 3 | 1167 | 0.85 | 0.87 | 113 | MG |
| 4 | 991 | 0.85 | 0.87 | 80 | MG, K |
| 5 | 1016 | 0.85 | 0.86 | 87 | MG |
Interfaces
41 interfaces between chains.
- A–L · 3292 Ų buried · 86 hydrogen bonds · protein-nucleic
- A–D · 3111 Ų buried · 89 hydrogen bonds · protein-nucleic
- A–I · 3061 Ų buried · 79 hydrogen bonds · protein-nucleic
- A–Q · 2747 Ų buried · 60 hydrogen bonds · protein-nucleic
- A–T · 2680 Ų buried · 67 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 13 modified (nucleotide modification, nonstandard).
Compared structures
- 4LF4 · Crystal Structure of 30S ribosomal subunit from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P80371
- Every structure of UniProt P80372
- Every structure of UniProt P80373
- Every structure of UniProt Q5SHQ5
- Every structure of UniProt Q5SLP8
- Every structure of UniProt P17291
- Every structure of UniProt Q5SHQ2
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt F6DEQ7
- Every structure of UniProt P80377
- Every structure of UniProt Q5SHQ1
- Every structure of UniProt Q5SJ76
- Every structure of UniProt Q5SJH3
- Every structure of UniProt Q5SHP7
- Every structure of UniProt Q5SLQ0
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P80380
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 4LF4 · PDBe 4LF4 · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt F6DEQ7 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt Q5SHP7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3
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